Hi Doug, Following the example in recon-all.log, I tried this: mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not open file On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log > file for an example command line that generates wmparc.mgz > > doug > > On 04/10/2014 09:52 AM, Corinna Bauer wrote: > > For creating corresponding wm segmentations to the rois derived from > > mris_divide_parcellation, should mri_aparc2wmseg be used or should I > > follow the steps outlined in this posting > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html > > ? > > > > Thanks > > > > Corinna > > > > > > On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer <corinna...@gmail.com > > <mailto:corinna...@gmail.com>> wrote: > > > > Perfect. Thanks! > > > > > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > > > > > > you'll need to figure it out from the volume itself by loading > > the seg > > with both -seg and -aux. When you find the label you want, > > click on it > > and the aux value in the control window will tell you what the > > id is > > > > doug > > > > On 04/09/2014 09:41 AM, Corinna Bauer wrote: > > > In the mri_extract_label, there is a label number. Where > > would I find > > > this for the new labels? > > > > > > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035 > > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii > > > > > > > > > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve > > > <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > yep, exactly > > > > > > > > > On 4/8/14 6:00 PM, Corinna Bauer wrote: > > >> Hi Doug, > > >> After I have the labels then in each subject's T1 > > space, I will > > >> need to then put them into diffusion and resting state > > space. > > >> > > >> I already have scripts that put the parcellations into > > >> subject-specific diffusion/resting state space (using > > bbregister, > > >> tkregister2, mri_vol2vol (using the inverse > > registration from > > >> bbregister to put the T1 into diffusion space), > > mri_extract_label > > >> (extract labels from aparc+aseg.mgz), and then > > mri_label2vol > > >> (register each of the extracted labels into diffusion > > space). > > >> Would a similar approach work for the new labels? > > >> > > >> Corinna > > >> > > >> > > >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve > > >> <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > >> > > >> > > >> Exactly what you have described won't work very > > well because > > >> it would be > > >> in the volume. I would divide up the parcellations in > > >> fsaverage space > > >> like you've done, then map the parcellation to each > > subject using > > >> mri_surf2surf (--sval-annot, see example 6) > > >> > > >> doug > > >> > > >> On 04/08/2014 04:54 PM, Corinna Bauer wrote: > > >> > Hello all, > > >> > > > >> > I am planning to use mris_divide_parcellation to > > split the > > >> Desikan > > >> > atlas into smaller ROIs, but will need the new > > ROIs to be > > >> consistent > > >> > between subjects. > > >> > > > >> > Can I achieve this if I register each subject to > > fsaverage > > >> space and > > >> > then apply the inverse transform to the divided > > >> parcellations (which > > >> > are currently done on the fsaverage brain)? > > >> > > > >> > If so, for extracting each label, what would be > > used for > > >> the label > > >> > number? > > >> > (i.e. mri_extract_label > > ${subj_dir}/mri/aparc+aseg.mgz *2035* > > >> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii) > > >> > > > >> > > > >> > Thanks > > >> > > > >> > Corinna > > >> > > > >> > > > >> > _______________________________________________ > > >> > Freesurfer mailing list > > >> > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> -- > > >> Douglas N. Greve, Ph.D. > > >> MGH-NMR Center > > >> gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > >> Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > >> Fax: 617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>> > > >> > > >> Bugs: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >> < > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >> Outgoing: > > >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> The information in this e-mail is intended only for > the > > >> person to whom it is > > >> addressed. If you believe this e-mail was sent to > > you in > > >> error and the e-mail > > >> contains patient information, please contact the > > Partners > > >> Compliance HelpLine at > > >> http://www.partners.org/complianceline . If the e-mail was > > >> sent to you in error > > >> but does not contain patient information, please > > contact the > > >> sender and properly > > >> dispose of the e-mail. > > >> > > >> > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > > sent to > > > you in error > > > but does not contain patient information, please contact > the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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